Hi, I am trying to perform DESeq2 for Kallisto. I ran Kallisto for 36 PE samples and got results files such as abundance.h5. Now I am trying DESeq2 analysis. I am getting everything correct but while making plotPCA it is making the plot of 6 samples. However, I have a total of 36 samples, I tried to find out the issue but not sure why the script taking only 6 samples for the analysis.
Here is the script:
files <- c("/DataAnalysis/270-aligned/abundance.h5", "/DataAnalysis/272-aligned/abundance.h5") ######just displaying 2 samples here, I have total 36 samples names(files) <- paste0("sample", 1:length(files)) txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE) head(txi.kallisto$counts) sampleTable <- data.frame(condition = factor(rep(c("mutant", "control"), each = 3))) rownames(sampleTable) <- colnames(countdata$counts) dds <- DESeqDataSetFromTximport(countdata, sampleTable, ~condition) #PCA plot vsd <- vst(dds) class(vsd) head(colData(vsd)) plotPCA(vsd, "condition")
> head(colData(vsd)) DataFrame with 6 rows and 1 column condition <factor> sample1 mutant sample2 mutant sample3 mutant sample4 control sample5 control sample6 control